Commit aa5b139c authored by Sander Bollen's avatar Sander Bollen
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vtools-filter docs

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Little toolset operating over VCF files. Uses cyvcf2 and cython under
the hood for speed.
### vtools-filter
Filter VCF files based on a few criteria. Will output both a filtered VCF
file, and a VCF file containing all the filtered-out variants.
#### Filter criteria
| name | meaning | optional |
| ---- | ------- | -------- |
| NON_CANONICAL | Non-canonical chromosome | Yes |
| INDEX_UNCALLED | Index uncalled or homozygous reference | Yes |
| TOO_HIGH_GONL_AF | Too high GonL allele frequency | Yes |
| TOO_HIGH_GNOMAD_AF | Too high GnomAD allele frequency | Yes |
| LOW_GQ | Too low GQ on index sample | Yes |
| DELETED_ALLELE | The only ALT allele is a deleted allele | No |
#### Configuration
Configuration of filters goes by a little JSON file. See [here]() for an
example, and [here]() for the json schema.
#### Usage
Usage: vtools-filter [OPTIONS]
-i, --input PATH Path to input VCF file [required]
-o, --output PATH Path to output (filtered) VCF file
-t, --trash PATH Path to trash VCF file [required]
-p, --params-file PATH Path to filter params json [required]
--index-sample TEXT Name of index sample [required]
--immediate-return / --no-immediate-return
Immediately write filters to file upon
hitting one filter criterium. Default = True
--help Show this message and exit.
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